Genome-wide analysis of the WD-repeat protein family in cucumber and Arabidopsis

Abstract

The WD-repeat (WDR) proteins comprise an astonishingly diverse superfamily of regulatory proteins. To date, genome-wide characterization of this family has only been conducted in Arabidopsis and little is known about WDR genes in cucumber (Cucumis sativus L.). This study identified 191 cucumber WDR genes in the latest cucumber genome and the CsWDR family contained a smaller number of identified genes compared to Arabidopsis. The results of this study were also supported by genome distribution and gene duplication analysis. Phylogenetic analysis showed that the WDR proteins could be classified into 21 subgroups. Moreover, an additional 12 AtWDR proteins were also identified and a complete overview of this gene family in Arabidopsis is presented, including the phylogeny, chromosome locations and duplication events. In addition, a comparative analysis between these genes in cucumber and Arabidopsis was performed and it suggested that there was strong gene conservation and that there was an expansion of particular functional genes during the evolution of the two species. The transcript abundance level analysis during abiotic stress (NaCl, ABA and low temperature treatments) identified six CsWDR genes that responded to one or more treatments. Tissue-specific expression profiles of these six genes were also analyzed. This study has produced a comparative genomics analysis of the WDR gene family in cucumber and Arabidopsis and provides the first steps towards the selection of CsWDR genes for cloning and functional dissection that can be used in further studies into their roles in cucumber stress resistance.

Genome-wide Analysis of WD40 Protein Family in Human

“…The pervasive but uneven distribution of hs WD40 genes on chromosomes is similar to those in plants202122, which may be correlated with different levels of segmental duplication on different chromosomes. For example, the high density of hs WD40 genes in chromosome 9 may be related to the enriched segmental duplications36, but further elucidation of these distribution patterns needs more detailed investigations.…”

“…Currently, several genome-wide studies have already put efforts on identifying and analysing WD40 protein family in plants including Arabidopsis, rice, foxtail millet, and cucumber19202122. These studies found variation in the number of WD40 genes in different plants, suggesting gene expansion history during evolution.…”

WD40‐REPEAT 5a represses root meristem growth by suppressing auxin synthesis through changes of nitric oxide accumulation in Arabidopsis

“…We noted that, although WDR5a is expressed in the stele (Figure 2C), previous reports indicated that NO mainly accumulates in the epidermal cells of the meristem and elongation zones, the lateral root cap and the cortex/ endodermal initial cells (Fern andez-Marcos et al, 2011). WDR5a, a member of the WD-repeat protein superfamily, may affect NO accumulation through its signal pathway, because this kind of protein can play roles through protein-protein interaction, either as a platform for the assembly of protein complexes or as a mediator of transient interplay among other proteins (Steven and Ludwig, 2003;Li et al, 2014). The detailed molecular mechanism underlying the role of WDR5a in suppressing TAA1 expression through increasing NO accumulation in the root meristem is worthy of further experimental exploration.…”

Assessment of Genetic Diversity, Population Structure, and Evolutionary Relationship of Uncharacterized Genes in a Novel Germplasm Collection of Diploid and Allotetraploid Gossypium Accessions Using EST and Genomic SSR Markers

“…We identified DUF819 (PF005684), which is not only highly conserved but also plays an important role against biotic and abiotic stress, among four sequenced cotton species by using the WDR (PF00400) superfamily as reference-genome-sequenced proteins. Genome-wide characterization of WD-repeats, also known as tryptophan-aspartic acid or the W-D superfamily, has only been conducted in Arabidopsis and Cucumber [49,50] till now. Therefore, a comprehensive study comprising a wide collection of germplasms, more efficient genotyping, and collective genomic platforms is required to measure the overall genetic diversity in diploid and allotetraploid cotton, which will help overcome the future challenges of the gene pool’s disastrous escape.…”